We have studied chromatin structure of regulated genes in several systems. Cloning of chromatin is possible in yeast - as a first example we have defined the structure of a minichromosome containing the TRP1/ARS1 fragment of yeast DN. Nine precisely phased nucleosomes are associated with the 1453 base pair length of DNA. In the year acid phosphatase gene, phased nucleosomes are present on the transcribed segment when the gene is inactive but phasing does not exist when the gene is actively transcribed. Regions outside the transcribed segment have phased nucleosomes in either case. For both genes, DNAse I hypersensitive sites are located near the 5' end of the gene when active transcription is occurring and absent when the gene is repressed. Qualitatively similar conclusions are made from studies of the early sea urchin histone genes during development. The basis for nucleosome phasing has been determined in one case, the association of histones with a cloned sea urchin DNA segment containing a 5S rRNA gene. Precise positioning of histones on DNA is determined by these two species alone. Detailed examination of this nucleosome reveals that the two DNA strands in the core particle are not identical in their interactions with histones.